SELECTED CANCER GENE EXPRESSION DIAGNOSTIC RELATED PAPERS
Ferles, C., Papanikolaou, Y. & Naidoo, K. J. Denoising Autoencoder Self-Organizing Map (DASOM). Neural Networks 105, 112-131, doi:https://doi.org/10.1016/j.neunet.2018.04.016 (2018).

Ferles, C., Papanikolaou, Y. & Naidoo, K. J. Cancer Types: RNA Sequencing Values from Tumor Samples/Tissues May 2018
DOI: 10.17632/sf5n64hydt.1

Ashkani, J. & Naidoo, K. J. Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes. Scientific Reports 6, 26451, doi:10.1038/srep26451 (2016).


SELECTED BIOINFORMATICS PAPERS
Suruzhon, M., Senapathi, T., Bodnarchuk, M. S., Viner, R., Wall, I. D., Barnett, C. B., Naidoo, K. J. & Essex, J. W. ProtoCaller: Robust Automation of Binding Free Energy Calculations. Journal of Chemical Information and Modeling 60, 1917-1921, doi:10.1021/acs.jcim.9b01158 (2020).

Senapathi, T., Bray, S., Barnett, C. B., Gruning, B. & Naidoo, K. J. Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). Bioinformatics 35, 3508-3509, doi:10.1093/bioinformatics/btz107 (2019).

Barnett, C. B., Aoki-Kinoshita, K. F. & Naidoo, K. J. The Glycome Analytics Platform: an integrative framework for glycobioinformatics. Bioinformatics 32, 3005-3011, doi:10.1093/bioinformatics/btw341 (2016).

SELECTED REACTION DYNAMICS PAPERS
Rogers, I. L. & Naidoo, K. J. Producing DFT/MM enzyme reaction trajectories from SCC-DFTB/MM driving forces to probe the underlying electronics of a glycosyltransferase reaction.
J Comput Chem 38, 1789-1798, doi:10.1002/jcc.24820 (2017).

Rogers, I. L. & Naidoo, K. J. Multidimensional Reaction Dynamics Reveal How the Enzyme TcTS Suppresses Competing Side Reactions and Their Side Products. ACS Catalysis, 6384-6392, doi:10.1021/acscatal.6b01522 (2016).

Govender, K., Gao, J. & Naidoo, K. J. AM1/d-CB1: A Semiempirical Model for QM/MM Simulations of Chemical Glycobiology Systems. Journal of Chemical Theory and Computation 10, 4694-4707, doi:10.1021/ct500372s (2014).

Renison, C. A., Fernandes, K. D. & Naidoo, K. J. Quantum supercharger library: Hyper-parallel integral derivatives algorithms for ab initioQM/MM dynamics. J. Comp. Chem. 36, 1410-1419, doi:10.1002/jcc.23938 (2015).

Crous, W., Field, M. J. & Naidoo, K. J. Simple Link Atom Saccharide Hybrid (SLASH) Treatment for Glycosidic Bonds at the QM/MM Boundary. Journal of Chemical Theory and Computation 10, 1727-1738, doi:10.1021/ct400903n (2014).